Data from: The Opiliones tree of life: shedding light on harvestmen relationships through transcriptomics

Opiliones are iconic arachnids with a Palaeozoic origin and a diversity that reflects ancient biogeographic patterns dating back at least to the times of Pangea. Owing to interest in harvestman diversity, evolution and biogeography, their relationships have been thoroughly studied using morphology and PCR-based Sanger approaches to infer their systematic relationships. More recently, two studies utilized transcriptomics-based phylogenomics to explore their basal relationships and diversification, but sampling was limiting for understanding deep evolutionary patterns, as they lacked good taxon representation at the family level. Here, we analysed a set of the 14 existing transcriptomes with 40 additional ones generated for this study, representing approximately 80% of the extant familial diversity in Opiliones. Our phylogenetic analyses, including a set of data matrices with different gene occupancy and evolutionary rates, and using a multitude of methods correcting for a diversity of factors affecting phylogenomic data matrices, provide a robust and stable Opiliones tree of life, where most families and higher taxa are precisely placed. Our dating analyses using alternative calibration points, methods and analytical parameters provide well-resolved old divergences, consistent with ancient regionalization in Pangea in some groups, and Pangean vicariance in others. The integration of state-of-the-art molecular techniques and analyses, together with the broadest taxonomic sampling to date presented in a phylogenomic study of harvestmen, provide new insights into harvestmen interrelationships, as well as an overview of the general biogeographic patterns of this ancient arthropod group.盲蛛（Opiliones）是一类具有古生代起源的标志性蛛形纲动物，其物种多样性所反映的古老生物地理格局至少可追溯至泛大陆（Pangea）形成时期。鉴于学界对盲蛛多样性、演化及生物地理学的研究兴趣，此前已有诸多研究借助形态学数据与基于聚合酶链式反应（PCR）的桑格（Sanger）测序方法，对其系统发育关系展开了深入探究。近年来，已有两项研究采用基于转录组（transcriptome）的系统发育组学手段，探索盲蛛的基部类群关系与分化模式，但由于科级类群采样不足，二者均难以阐明其深层演化格局。本研究整合了14套已公开的转录组数据，并新增40套本次实验生成的转录组数据，涵盖了现存盲蛛约80%的科级类群多样性。我们构建了多套包含不同基因占比与进化速率的数据集矩阵，并采用多种校正方法以抵消影响系统发育组数据矩阵的各类干扰因素，最终得到了稳健且稳定的盲蛛生命之树，绝大多数科级及以上类群的系统发育位置均得到了精准解析。我们通过多种校准位点、分析方法与参数设置开展年代学分析，得到了分辨率良好的古老分化时间估计结果：部分类群的分化与泛大陆时期的古地理分区相吻合，另一部分类群则符合泛大陆隔离分化（vicariance）模式。本研究将前沿分子实验技术与分析方法相结合，同时实现了盲蛛系统发育组学研究迄今为止最全面的类群采样，不仅为阐明盲蛛的类群间亲缘关系提供了全新视角，也为这一古老节肢动物类群的整体生物地理格局研究提供了系统性参考。